I am having the same issue. No matter how I alter the body of the email for estimates and sales orders I send it will just send with the default. I do not have access to change the template for each email nor is that practical. What's interesting is even if I delete the attachment on the email before I send it, the attachment will still send! 

It's frustrating to me that QB has been sidestepping the issue in the replies to the comments or sending their paying customers to another company that has nothing to do with the issue. Please provide an update and take responsibility. This is ridiculous.